Introduction

Data from RAB : CD8+ T cells from mice

Mrpl28KO cells Trpn vs Trpp

Volcano plot

Getting some stats yay

table(res_tbl$padj<=0.05) # significant genes
## 
## FALSE  TRUE 
## 13468  2793
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange<=-1) # signif and downreg
## 
## FALSE  TRUE 
## 21694  1048
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange>=1) # signif and upreg
## 
## FALSE  TRUE 
## 23015   474

GSEA analysis logFc

Gene ontology

ID setSize enrichmentScore NES pvalue p.adjust qvalue
GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS 65 0.5135850 2.625708 0.0000000 0.0000361 0.0000342
GOBP_RIBOSOME_BIOGENESIS 55 0.5127551 2.527026 0.0000003 0.0003136 0.0002978
GOBP_MITOTIC_SISTER_CHROMATID_SEGREGATION 37 -0.5985647 -2.239727 0.0000024 0.0010616 0.0010082
GOBP_NCRNA_METABOLIC_PROCESS 96 0.3892952 2.169905 0.0000021 0.0010616 0.0010082
GOBP_RRNA_METABOLIC_PROCESS 47 0.5117327 2.421799 0.0000047 0.0016904 0.0016054
GOBP_SISTER_CHROMATID_SEGREGATION 42 -0.5681298 -2.181695 0.0000177 0.0052972 0.0050308
GOBP_TRNA_METABOLIC_PROCESS 40 0.5028682 2.303527 0.0000360 0.0092533 0.0087880
GOBP_NCRNA_PROCESSING 67 0.4108794 2.128387 0.0000582 0.0131006 0.0124417
GOBP_NUCLEAR_CHROMOSOME_SEGREGATION 55 -0.4958367 -2.013524 0.0001171 0.0234258 0.0222477
GOBP_MITOCHONDRIAL_GENE_EXPRESSION 33 0.5081217 2.210067 0.0001798 0.0323711 0.0307430
GOBP_CHROMOSOME_SEGREGATION 64 -0.4594266 -1.922331 0.0002869 0.0397294 0.0377313
GOBP_MITOTIC_NUCLEAR_DIVISION 61 -0.4604111 -1.908086 0.0002769 0.0397294 0.0377313
GOBP_ORGANELLE_FISSION 94 -0.4180756 -1.866564 0.0002468 0.0397294 0.0377313

Reactome

ID setSize enrichmentScore NES pvalue p.adjust qvalue
REACTOME_TRANSLATION 79 0.5295162 2.869118 0.0000000 0.0000000 0.0000000
REACTOME_METABOLISM_OF_RNA 117 0.4223805 2.459842 0.0000000 0.0000010 0.0000008
REACTOME_CELLULAR_RESPONSES_TO_STIMULI 129 0.4014826 2.377490 0.0000000 0.0000010 0.0000008
REACTOME_RRNA_PROCESSING 48 0.5166074 2.500918 0.0000011 0.0000968 0.0000748
REACTOME_EUKARYOTIC_TRANSLATION_INITIATION 36 0.5072457 2.286372 0.0000576 0.0034968 0.0027007
REACTOME_SELENOAMINO_ACID_METABOLISM 35 0.5082572 2.270637 0.0000724 0.0034968 0.0027007
REACTOME_CELLULAR_RESPONSE_TO_STARVATION 42 0.4775702 2.232308 0.0000664 0.0034968 0.0027007
REACTOME_REGULATION_OF_CHOLESTEROL_BIOSYNTHESIS_BY_SREBP_SREBF 21 -0.6257007 -2.052393 0.0001412 0.0059674 0.0046089
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES 75 0.3702559 1.977678 0.0001649 0.0061933 0.0047833
REACTOME_TRNA_PROCESSING 15 0.6543078 2.261748 0.0002036 0.0066801 0.0051593
REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY 33 0.5056563 2.226401 0.0002183 0.0066801 0.0051593
REACTOME_CELLULAR_RESPONSE_TO_CHEMICAL_STRESS 28 0.5154562 2.157966 0.0002965 0.0066801 0.0051593
REACTOME_NONSENSE_MEDIATED_DECAY_NMD 30 0.5023715 2.151307 0.0002780 0.0066801 0.0051593
REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 30 0.5023715 2.151307 0.0002780 0.0066801 0.0051593
REACTOME_REGULATION_OF_EXPRESSION_OF_SLITS_AND_ROBOS 48 0.4333158 2.097700 0.0002382 0.0066801 0.0051593
REACTOME_MITOCHONDRIAL_TRANSLATION 24 0.5488855 2.196677 0.0004284 0.0090491 0.0069891
REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE 10 -0.7398369 -1.968646 0.0004718 0.0093808 0.0072452
REACTOME_ACTIVATION_OF_GENE_EXPRESSION_BY_SREBF_SREBP 20 -0.6157462 -1.995155 0.0005296 0.0099438 0.0076800
REACTOME_SIGNALING_BY_ROBO_RECEPTORS 55 0.3734654 1.871865 0.0008098 0.0144063 0.0111266
REACTOME_PROTEIN_LOCALIZATION 27 0.5024540 2.088634 0.0009498 0.0160517 0.0123975
REACTOME_CYTOPROTECTION_BY_HMOX1 21 0.5466719 2.090293 0.0010955 0.0163131 0.0125993
REACTOME_RESPONSE_OF_EIF2AK1_HRI_TO_HEME_DEFICIENCY 10 0.6900999 2.055247 0.0011583 0.0163131 0.0125993
REACTOME_INFLUENZA_INFECTION 31 0.4689805 2.033479 0.0011376 0.0163131 0.0125993
REACTOME_METABOLISM_OF_STEROIDS 39 -0.4921693 -1.867084 0.0010562 0.0163131 0.0125993
REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT 22 0.5390071 2.098177 0.0012485 0.0168796 0.0130369
REACTOME_ABC_TRANSPORTER_DISORDERS 21 0.5387948 2.060174 0.0014062 0.0173324 0.0133866
REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION 26 0.5015785 2.055421 0.0013818 0.0173324 0.0133866
REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S 20 0.5395258 2.034482 0.0014871 0.0173324 0.0133866
REACTOME_DEFECTIVE_CFTR_CAUSES_CYSTIC_FIBROSIS 20 0.5385827 2.030925 0.0014871 0.0173324 0.0133866
REACTOME_TRNA_AMINOACYLATION 13 0.6109148 2.010038 0.0022598 0.0254606 0.0196643
REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT 13 0.6066811 1.996108 0.0026433 0.0276663 0.0213679
REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX 17 0.5458120 1.953290 0.0029724 0.0276663 0.0213679
REACTOME_G1_S_DNA_DAMAGE_CHECKPOINTS 17 0.5458120 1.953290 0.0029724 0.0276663 0.0213679
REACTOME_ORC1_REMOVAL_FROM_CHROMATIN 17 0.5458120 1.953290 0.0029724 0.0276663 0.0213679
REACTOME_REGULATION_OF_RUNX3_EXPRESSION_AND_ACTIVITY 17 0.5458120 1.953290 0.0029724 0.0276663 0.0213679
REACTOME_STABILIZATION_OF_P53 17 0.5458120 1.953290 0.0029724 0.0276663 0.0213679
REACTOME_CHOLESTEROL_BIOSYNTHESIS 18 -0.5910818 -1.862827 0.0030286 0.0276663 0.0213679
REACTOME_DECTIN_1_MEDIATED_NONCANONICAL_NF_KB_SIGNALING 19 0.5462416 2.029126 0.0033957 0.0286841 0.0221540
REACTOME_REGULATION_OF_HMOX1_EXPRESSION_AND_ACTIVITY 19 0.5462416 2.029126 0.0033957 0.0286841 0.0221540
REACTOME_SWITCHING_OF_ORIGINS_TO_A_POST_REPLICATIVE_STATE 19 0.5462416 2.029126 0.0033957 0.0286841 0.0221540
REACTOME_PHASE_I_FUNCTIONALIZATION_OF_COMPOUNDS 20 -0.5731167 -1.857026 0.0035643 0.0286841 0.0221540
REACTOME_HIV_INFECTION 44 0.3779156 1.799713 0.0034870 0.0286841 0.0221540
REACTOME_PERK_REGULATES_GENE_EXPRESSION 12 0.6216641 1.991665 0.0037666 0.0296069 0.0228667
REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES 11 -0.6549914 -1.793434 0.0039689 0.0300735 0.0232271
REACTOME_ION_CHANNEL_TRANSPORT 27 -0.5108532 -1.777328 0.0040039 0.0300735 0.0232271
REACTOME_HEDGEHOG_LIGAND_BIOGENESIS 19 0.5383707 1.999888 0.0044970 0.0330430 0.0255206
REACTOME_TRANSCRIPTION_OF_THE_HIV_GENOME 12 0.6163605 1.974673 0.0046879 0.0337127 0.0260378
REACTOME_AUF1_HNRNP_D0_BINDS_AND_DESTABILIZES_MRNA 16 0.5455975 1.921696 0.0056962 0.0377513 0.0291570
REACTOME_NEGATIVE_REGULATION_OF_NOTCH4_SIGNALING 16 0.5455975 1.921696 0.0056962 0.0377513 0.0291570
REACTOME_REGULATION_OF_PTEN_STABILITY_AND_ACTIVITY 16 0.5455975 1.921696 0.0056962 0.0377513 0.0291570
REACTOME_SCF_SKP2_MEDIATED_DEGRADATION_OF_P27_P21 16 0.5455975 1.921696 0.0056962 0.0377513 0.0291570
REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES 15 0.5453831 1.885227 0.0061709 0.0401111 0.0309796
REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION 11 0.6104355 1.895143 0.0066647 0.0425034 0.0328273
REACTOME_ATF4_ACTIVATES_GENES_IN_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS 10 0.6309804 1.879178 0.0071798 0.0449401 0.0347093
REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION 26 -0.5054343 -1.744175 0.0076230 0.0468468 0.0361819

Wikipathways

ID setSize enrichmentScore NES pvalue p.adjust qvalue
WP_CHOLESTEROL_BIOSYNTHESIS_PATHWAY 14 -0.7126544 -2.091174 0.0000882 0.0144723 0.0135620
WP_STEROL_REGULATORY_ELEMENTBINDING_PROTEINS_SREBP_SIGNALING 21 -0.6237551 -2.055265 0.0003726 0.0305505 0.0286288
WP_CHOLESTEROL_METABOLISM_WITH_BLOCH_AND_KANDUTSCHRUSSELL_PATHWAYS 27 -0.5716347 -1.999788 0.0006165 0.0337021 0.0315822

Perturbations

ID setSize enrichmentScore NES pvalue p.adjust font.size
HOUNKPE_HOUSEKEEPING_GENES 188 0.4665197 2.961383 0.0e+00 0.0000001 0.0000001
FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_DN 75 -0.6039023 -2.611669 0.0e+00 0.0000001 0.0000001
FISCHER_G2_M_CELL_CYCLE 86 -0.5338579 -2.351550 0.0e+00 0.0000014 0.0000013
ODONNELL_TFRC_TARGETS_DN 42 -0.6457153 -2.457699 0.0e+00 0.0000068 0.0000060
GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN 10 0.8857221 2.657281 0.0e+00 0.0000072 0.0000064
IBRAHIM_NRF1_UP 87 0.4492715 2.472885 0.0e+00 0.0000120 0.0000106
GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP 149 -0.4373462 -2.097099 2.0e-07 0.0000488 0.0000431
MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 152 -0.4281863 -2.058851 6.0e-07 0.0001252 0.0001104
ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER 45 -0.5897654 -2.298622 9.0e-07 0.0001661 0.0001465
BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUENZA_A_DEL_NS1_INFECTION_DN 63 -0.5318264 -2.220798 1.1e-06 0.0001838 0.0001621
MEBARKI_HCC_PROGENITOR_FZD8CRD_UP 128 -0.4338369 -2.041815 2.4e-06 0.0003532 0.0003115
IBRAHIM_NRF2_UP 122 0.3480958 2.031707 2.8e-06 0.0003743 0.0003302
CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN 14 -0.7725172 -2.243823 5.5e-06 0.0006782 0.0005982
GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN 11 0.8024689 2.461662 7.1e-06 0.0008117 0.0007159
WILCOX_RESPONSE_TO_PROGESTERONE_UP 53 -0.5315907 -2.160401 8.1e-06 0.0008604 0.0007589

Hallmarks

ID setSize enrichmentScore NES pvalue p.adjust qvalue
HALLMARK_MYC_TARGETS_V1 33 0.4928529 2.136054 0.0005568 0.0122487 0.0099631
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 28 0.5087449 2.111494 0.0005461 0.0122487 0.0099631
HALLMARK_KRAS_SIGNALING_DN 30 -0.5345642 -1.926403 0.0011950 0.0131450 0.0106921
HALLMARK_HYPOXIA 57 0.3809432 1.925217 0.0011454 0.0131450 0.0106921

ORA

GOBP

ID GeneRatio p.adjust qvalue
GOBP_STEROL_METABOLIC_PROCESS 34/1112 0.0000054 0.0000051
GOBP_STEROL_BIOSYNTHETIC_PROCESS 20/1112 0.0000076 0.0000071
GOBP_MITOTIC_NUCLEAR_DIVISION 47/1112 0.0001141 0.0001065
GOBP_SECONDARY_ALCOHOL_METABOLIC_PROCESS 30/1112 0.0001141 0.0001065
GOBP_MITOTIC_SISTER_CHROMATID_SEGREGATION 32/1112 0.0002413 0.0002253
GOBP_STEROID_BIOSYNTHETIC_PROCESS 32/1112 0.0002413 0.0002253
GOBP_SISTER_CHROMATID_SEGREGATION 35/1112 0.0002531 0.0002363
GOBP_ORGANELLE_FISSION 65/1112 0.0003312 0.0003092
GOBP_STEROID_METABOLIC_PROCESS 47/1112 0.0003312 0.0003092
GOBP_REGULATION_OF_MITOTIC_NUCLEAR_DIVISION 23/1112 0.0011667 0.0010893
GOBP_NUCLEAR_CHROMOSOME_SEGREGATION 42/1112 0.0011667 0.0010893
GOBP_ORGANIC_HYDROXY_COMPOUND_BIOSYNTHETIC_PROCESS 36/1112 0.0036209 0.0033808
GOBP_CHROMOSOME_SEGREGATION 46/1112 0.0052635 0.0049145
GOBP_ISOPRENOID_BIOSYNTHETIC_PROCESS 10/1112 0.0080416 0.0075084
GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME_CENTROMERIC_REGION 9/1112 0.0095109 0.0088803
GOBP_REGULATION_OF_NUCLEAR_DIVISION 24/1112 0.0102748 0.0095935
GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS 40/1112 0.0179359 0.0167467
GOBP_ALCOHOL_METABOLIC_PROCESS 44/1112 0.0195397 0.0182441
GOBP_EPITHELIAL_CELL_CELL_ADHESION 7/1112 0.0209312 0.0195433
GOBP_CELL_ADHESION_MEDIATED_BY_INTEGRIN 17/1112 0.0209312 0.0195433
GOBP_ACTOMYOSIN_STRUCTURE_ORGANIZATION 29/1112 0.0209312 0.0195433
GOBP_ISOPRENOID_METABOLIC_PROCESS 19/1112 0.0353170 0.0329753
GOBP_PROTEIN_LOCALIZATION_TO_CONDENSED_CHROMOSOME 7/1112 0.0407209 0.0380209 
## [1] 23  9

Reactome

ID GeneRatio p.adjust qvalue
REACTOME_CHOLESTEROL_BIOSYNTHESIS 14/741 0.0000003 0.0000003
REACTOME_ACTIVATION_OF_GENE_EXPRESSION_BY_SREBF_SREBP 16/741 0.0000130 0.0000129
REACTOME_REGULATION_OF_CHOLESTEROL_BIOSYNTHESIS_BY_SREBP_SREBF 17/741 0.0000994 0.0000981
REACTOME_METABOLISM_OF_STEROIDS 30/741 0.0001130 0.0001114
REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION 22/741 0.0036959 0.0036448
REACTOME_KINESINS 13/741 0.0227502 0.0224359
REACTOME_RESOLUTION_OF_SISTER_CHROMATID_COHESION 21/741 0.0264347 0.0260695
REACTOME_BASIGIN_INTERACTIONS 8/741 0.0366839 0.0361771
REACTOME_RHO_GTPASES_ACTIVATE_FORMINS 22/741 0.0369833 0.0364723 
## [1] 9 9

Specific pathways signatures

The oxphos signature

Highlight on the volcano plot of the genes found to be implicated in oxphos + table

gene log2FoldChange padj description
Ak4 1.2455168 0.0020104 adenylate kinase 4 [Source:MGI Symbol;Acc:MGI:87979]
Atpsckmt 0.8206306 0.0090980 ATP synthase C subunit lysine N-methyltransferase [Source:MGI Symbol;Acc:MGI:1915323]
Cdk1 -1.4188456 0.0232454 cyclin-dependent kinase 1 [Source:MGI Symbol;Acc:MGI:88351]
Chchd10 1.5351733 0.0001042 coiled-coil-helix-coiled-coil-helix domain containing 10 [Source:MGI Symbol;Acc:MGI:2143558]
Cox6a2 2.7373563 0.0000000 cytochrome c oxidase subunit 6A2 [Source:MGI Symbol;Acc:MGI:104649]
Dnajc15 1.0745517 0.0009153 DnaJ heat shock protein family (Hsp40) member C15 [Source:MGI Symbol;Acc:MGI:1913398]
Mlxipl -2.2526155 0.0412009 MLX interacting protein-like [Source:MGI Symbol;Acc:MGI:1927999]
Ndufa2 0.8619382 0.0044294 NADH:ubiquinone oxidoreductase subunit A2 [Source:MGI Symbol;Acc:MGI:1343103]
Ndufb7 0.6055806 0.0237741 NADH:ubiquinone oxidoreductase subunit B7 [Source:MGI Symbol;Acc:MGI:1914166]
Nupr1 2.1440091 0.0000000 nuclear protein transcription regulator 1 [Source:MGI Symbol;Acc:MGI:1891834]
Shmt2 1.0733335 0.0093724 serine hydroxymethyltransferase 2 (mitochondrial) [Source:MGI Symbol;Acc:MGI:1277989]
Slc25a23 -1.4187696 0.0000538 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23 [Source:MGI Symbol;Acc:MGI:1914222]
Slc25a33 0.8672362 0.0194129 solute carrier family 25, member 33 [Source:MGI Symbol;Acc:MGI:1917806]
Tefm 0.9089343 0.0106374 transcription elongation factor, mitochondrial [Source:MGI Symbol;Acc:MGI:1915800]
Uqcc2 0.5460583 0.0461549 ubiquinol-cytochrome c reductase complex assembly factor 2 [Source:MGI Symbol;Acc:MGI:1914517]
Uqcrh -1.4807298 0.0000004 ubiquinol-cytochrome c reductase hinge protein [Source:MGI Symbol;Acc:MGI:1913826]
Uqcrq 1.0972648 0.0000712 ubiquinol-cytochrome c reductase, complex III subunit VII [Source:MGI Symbol;Acc:MGI:107807]

GSEA on filtered terms from GO, Reactome, Hallmark

The glycolytic process

Highlight on the volcano plot of the genes found to be implicated in oxphos + table

gene log2FoldChange padj description
Aldoa 0.8021707 0.0154322 aldolase A, fructose-bisphosphate [Source:MGI Symbol;Acc:MGI:87994]
Aldoc -1.1891393 0.0034874 aldolase C, fructose-bisphosphate [Source:MGI Symbol;Acc:MGI:101863]
App 1.6092435 0.0278673 amyloid beta (A4) precursor protein [Source:MGI Symbol;Acc:MGI:88059]
Cbfa2t3 -2.5089684 0.0046741 CBFA2/RUNX1 translocation partner 3 [Source:MGI Symbol;Acc:MGI:1338013]
Eif6 0.9475136 0.0283347 eukaryotic translation initiation factor 6 [Source:MGI Symbol;Acc:MGI:1196288]
Eno1 0.9890876 0.0416842 enolase 1, alpha non-neuron [Source:MGI Symbol;Acc:MGI:95393]
Eno2 -1.4500608 0.0000152 enolase 2, gamma neuronal [Source:MGI Symbol;Acc:MGI:95394]
Gale -1.1604461 0.0003816 galactose-4-epimerase, UDP [Source:MGI Symbol;Acc:MGI:1921496]
Gpd1 -2.3125488 0.0463671 glycerol-3-phosphate dehydrogenase 1 (soluble) [Source:MGI Symbol;Acc:MGI:95679]
Hdac4 0.8700445 0.0002511 histone deacetylase 4 [Source:MGI Symbol;Acc:MGI:3036234]
Hif1a 0.7502141 0.0047334 hypoxia inducible factor 1, alpha subunit [Source:MGI Symbol;Acc:MGI:106918]
Mlxipl -2.2526155 0.0412009 MLX interacting protein-like [Source:MGI Symbol;Acc:MGI:1927999]
Nupr1 2.1440091 0.0000000 nuclear protein transcription regulator 1 [Source:MGI Symbol;Acc:MGI:1891834]
Ogt 0.8941027 0.0125438 O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) [Source:MGI Symbol;Acc:MGI:1339639]
Pfkl 1.0534047 0.0129213 phosphofructokinase, liver, B-type [Source:MGI Symbol;Acc:MGI:97547]
Pfkm -0.7126608 0.0010524 phosphofructokinase, muscle [Source:MGI Symbol;Acc:MGI:97548]
Pgam1 0.9195703 0.0129445 phosphoglycerate mutase 1 [Source:MGI Symbol;Acc:MGI:97552]
Prxl2c 1.5777496 0.0002694 peroxiredoxin like 2C [Source:MGI Symbol;Acc:MGI:1913379]
Sirt6 0.7663040 0.0003463 sirtuin 6 [Source:MGI Symbol;Acc:MGI:1354161]
Slc2a6 -2.1096609 0.0000002 solute carrier family 2 (facilitated glucose transporter), member 6 [Source:MGI Symbol;Acc:MGI:2443286]
Tpi1 1.4474463 0.0075150 triosephosphate isomerase 1 [Source:MGI Symbol;Acc:MGI:98797]

The myc signature

Highlight on the volcano plot of the genes found to be implicated in oxphos + table

gene log2FoldChange padj description
Acss2 -2.2568689 0.0000000 acyl-CoA synthetase short-chain family member 2 [Source:MGI Symbol;Acc:MGI:1890410]
Smtn -2.6718368 0.0000000 smoothelin [Source:MGI Symbol;Acc:MGI:1354727]
Tgm2 2.9732904 0.0000000 transglutaminase 2, C polypeptide [Source:MGI Symbol;Acc:MGI:98731]
Sorl1 -1.2988757 0.0000000 sortilin-related receptor, LDLR class A repeats-containing [Source:MGI Symbol;Acc:MGI:1202296]
Ptrh2 1.5938624 0.0000000 peptidyl-tRNA hydrolase 2 [Source:MGI Symbol;Acc:MGI:2444848]
Ddah2 -2.0404624 0.0000000 dimethylarginine dimethylaminohydrolase 2 [Source:MGI Symbol;Acc:MGI:1859016]
Ciart 1.8653598 0.0000001 circadian associated repressor of transcription [Source:MGI Symbol;Acc:MGI:2684975]
Emp1 -1.8546138 0.0000024 epithelial membrane protein 1 [Source:MGI Symbol;Acc:MGI:107941]
Flnb -1.1047019 0.0000040 filamin, beta [Source:MGI Symbol;Acc:MGI:2446089]
Als2cl -1.2855512 0.0000050 ALS2 C-terminal like [Source:MGI Symbol;Acc:MGI:2447532]
Plekhg2 -1.3882211 0.0000477 pleckstrin homology domain containing, family G (with RhoGef domain) member 2 [Source:MGI Symbol;Acc:MGI:2141874]
Mettl1 1.8870013 0.0000626 methyltransferase like 1 [Source:MGI Symbol;Acc:MGI:1339986]
Ipo4 1.0987514 0.0000950 importin 4 [Source:MGI Symbol;Acc:MGI:1923001]
Sord -1.0533414 0.0002907 sorbitol dehydrogenase [Source:MGI Symbol;Acc:MGI:98266]
Atp2b4 -1.2534448 0.0002938 ATPase, Ca++ transporting, plasma membrane 4 [Source:MGI Symbol;Acc:MGI:88111]
Plau -2.4797085 0.0003452 plasminogen activator, urokinase [Source:MGI Symbol;Acc:MGI:97611]
Pfkm -0.7126608 0.0010524 phosphofructokinase, muscle [Source:MGI Symbol;Acc:MGI:97548]
Wdr74 1.1017039 0.0012277 WD repeat domain 74 [Source:MGI Symbol;Acc:MGI:2147427]
Trmt1 0.6657382 0.0013367 tRNA methyltransferase 1 [Source:MGI Symbol;Acc:MGI:1289155]
Ddx28 0.8281961 0.0020593 DEAD box helicase 28 [Source:MGI Symbol;Acc:MGI:1919236]
Flad1 0.6821690 0.0030943 flavin adenine dinucleotide synthetase 1 [Source:MGI Symbol;Acc:MGI:2443030]
Scfd2 0.7358560 0.0031311 Sec1 family domain containing 2 [Source:MGI Symbol;Acc:MGI:2443446]
Vmp1 0.7937707 0.0040844 vacuole membrane protein 1 [Source:MGI Symbol;Acc:MGI:1923159]
Farsb 0.9689679 0.0065456 phenylalanyl-tRNA synthetase, beta subunit [Source:MGI Symbol;Acc:MGI:1346035]
Akap12 -1.0646350 0.0067997 A kinase (PRKA) anchor protein (gravin) 12 [Source:MGI Symbol;Acc:MGI:1932576]
Ubiad1 0.7201655 0.0071640 UbiA prenyltransferase domain containing 1 [Source:MGI Symbol;Acc:MGI:1918957]
Prr5 -0.8632664 0.0084843 proline rich 5 (renal) [Source:MGI Symbol;Acc:MGI:1924714]
Ddx10 0.7835497 0.0097780 DEAD box helicase 10 [Source:MGI Symbol;Acc:MGI:1924841]
Ccng2 -0.8565674 0.0098738 cyclin G2 [Source:MGI Symbol;Acc:MGI:1095734]
Runx1 -1.3021025 0.0108069 runt related transcription factor 1 [Source:MGI Symbol;Acc:MGI:99852]
Wsb1 -0.5580024 0.0109492 WD repeat and SOCS box-containing 1 [Source:MGI Symbol;Acc:MGI:1926139]
Gpatch4 1.2088627 0.0155572 G patch domain containing 4 [Source:MGI Symbol;Acc:MGI:1913864]
Mknk1 0.6168437 0.0169112 MAP kinase-interacting serine/threonine kinase 1 [Source:MGI Symbol;Acc:MGI:894316]
Triobp 0.6055288 0.0171502 TRIO and F-actin binding protein [Source:MGI Symbol;Acc:MGI:1349410]
Mical1 -0.6886807 0.0178766 microtubule associated monooxygenase, calponin and LIM domain containing 1 [Source:MGI Symbol;Acc:MGI:2385847]
Erbb3 -0.8495559 0.0194129 erb-b2 receptor tyrosine kinase 3 [Source:MGI Symbol;Acc:MGI:95411]
Srm 1.0816983 0.0211371 spermidine synthase [Source:MGI Symbol;Acc:MGI:102690]
Eef1akmt4 1.1230263 0.0230284 EEF1A lysine methyltransferase 4 [Source:MGI Symbol;Acc:MGI:5903914]
Kcnq5 0.6728705 0.0261223 potassium voltage-gated channel, subfamily Q, member 5 [Source:MGI Symbol;Acc:MGI:1924937]
Ssh3 -0.9606735 0.0269862 slingshot protein phosphatase 3 [Source:MGI Symbol;Acc:MGI:2683546]
Npm1 0.6583986 0.0283545 nucleophosmin 1 [Source:MGI Symbol;Acc:MGI:106184]
Lsg1 0.6602971 0.0294506 large 60S subunit nuclear export GTPase 1 [Source:MGI Symbol;Acc:MGI:107236]
Ncl 0.7910950 0.0327407 nucleolin [Source:MGI Symbol;Acc:MGI:97286]
Paics -0.6215554 0.0337196 phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoribosylaminoimidazole, succinocarboxamide synthetase [Source:MGI Symbol;Acc:MGI:1914304]
Imp4 0.6598715 0.0392094 IMP4, U3 small nucleolar ribonucleoprotein [Source:MGI Symbol;Acc:MGI:106572]
Nop2 0.8184044 0.0447663 NOP2 nucleolar protein [Source:MGI Symbol;Acc:MGI:107891]
Tgm1 -1.5296412 0.0469190 transglutaminase 1, K polypeptide [Source:MGI Symbol;Acc:MGI:98730]
Hspd1 0.7346068 0.0479096 heat shock protein 1 (chaperonin) [Source:MGI Symbol;Acc:MGI:96242]
Ercc1 0.6338760 0.0496072 excision repair cross-complementing rodent repair deficiency, complementation group 1 [Source:MGI Symbol;Acc:MGI:95412]

Pattern search in data

Slcxxx transporters

gene log2FoldChange padj description
Slc10a3 1.0615228 0.0029152 solute carrier family 10 (sodium/bile acid cotransporter family), member 3 [Source:MGI Symbol;Acc:MGI:95048]
Slc10a7 0.7621711 0.0086652 solute carrier family 10 (sodium/bile acid cotransporter family), member 7 [Source:MGI Symbol;Acc:MGI:1924025]
Slc11a2 -0.6036144 0.0261223 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 [Source:MGI Symbol;Acc:MGI:1345279]
Slc14a1 -2.7640296 0.0000974 solute carrier family 14 (urea transporter), member 1 [Source:MGI Symbol;Acc:MGI:1351654]
Slc15a1 -5.2481326 0.0000000 solute carrier family 15 (oligopeptide transporter), member 1 [Source:MGI Symbol;Acc:MGI:1861376]
Slc16a3 1.2470158 0.0034741 solute carrier family 16 (monocarboxylic acid transporters), member 3 [Source:MGI Symbol;Acc:MGI:1933438]
Slc1a2 -2.3209408 0.0087233 solute carrier family 1 (glial high affinity glutamate transporter), member 2 [Source:MGI Symbol;Acc:MGI:101931]
Slc1a4 1.3486491 0.0000037 solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 [Source:MGI Symbol;Acc:MGI:2135601]
Slc1a5 0.6126271 0.0203806 solute carrier family 1 (neutral amino acid transporter), member 5 [Source:MGI Symbol;Acc:MGI:105305]
Slc25a1 -1.1896109 0.0000137 solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1 [Source:MGI Symbol;Acc:MGI:1345283]
Slc25a15 0.7708455 0.0081739 solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15 [Source:MGI Symbol;Acc:MGI:1342274]
Slc25a20 0.5879487 0.0238877 solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20 [Source:MGI Symbol;Acc:MGI:1928738]
Slc25a23 -1.4187696 0.0000538 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23 [Source:MGI Symbol;Acc:MGI:1914222]
Slc25a25 -0.7660400 0.0418809 solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25 [Source:MGI Symbol;Acc:MGI:1915913]
Slc25a30 -0.8739697 0.0019587 solute carrier family 25, member 30 [Source:MGI Symbol;Acc:MGI:1914804]
Slc25a33 0.8672362 0.0194129 solute carrier family 25, member 33 [Source:MGI Symbol;Acc:MGI:1917806]
Slc25a5 -0.8637030 0.0036617 solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5 [Source:MGI Symbol;Acc:MGI:1353496]
Slc26a11 -1.1359541 0.0074989 solute carrier family 26, member 11 [Source:MGI Symbol;Acc:MGI:2444589]
Slc28a2b -2.2569328 0.0003818 solute carrier family 28 member 2b [Source:MGI Symbol;Acc:MGI:3702173]
Slc2a1 1.4609837 0.0000000 solute carrier family 2 (facilitated glucose transporter), member 1 [Source:MGI Symbol;Acc:MGI:95755]
Slc2a4 -3.1078641 0.0210463 solute carrier family 2 (facilitated glucose transporter), member 4 [Source:MGI Symbol;Acc:MGI:95758]
Slc2a5 3.0017119 0.0454414 solute carrier family 2 (facilitated glucose transporter), member 5 [Source:MGI Symbol;Acc:MGI:1928369]
Slc2a6 -2.1096609 0.0000002 solute carrier family 2 (facilitated glucose transporter), member 6 [Source:MGI Symbol;Acc:MGI:2443286]
Slc35b1 0.6270930 0.0108831 solute carrier family 35, member B1 [Source:MGI Symbol;Acc:MGI:1343133]
Slc35b2 -0.7789463 0.0081476 solute carrier family 35, member B2 [Source:MGI Symbol;Acc:MGI:1921086]
Slc35b3 0.8985752 0.0000612 solute carrier family 35, member B3 [Source:MGI Symbol;Acc:MGI:1913978]
Slc35b4 0.5768558 0.0317071 solute carrier family 35, member B4 [Source:MGI Symbol;Acc:MGI:1931249]
Slc36a3os -1.1035583 0.0421059 solute carrier family 36 (proton/amino acid symporter), member 3, opposite strand [Source:MGI Symbol;Acc:MGI:3651340]
Slc38a7 1.2911585 0.0001323 solute carrier family 38, member 7 [Source:MGI Symbol;Acc:MGI:2679005]
Slc39a10 -1.9087591 0.0000026 solute carrier family 39 (zinc transporter), member 10 [Source:MGI Symbol;Acc:MGI:1914515]
Slc39a11 0.5284754 0.0237358 solute carrier family 39 (metal ion transporter), member 11 [Source:MGI Symbol;Acc:MGI:1917056]
Slc39a3 0.8969635 0.0014031 solute carrier family 39 (zinc transporter), member 3 [Source:MGI Symbol;Acc:MGI:2147269]
Slc3a2 1.1014104 0.0000073 solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 [Source:MGI Symbol;Acc:MGI:96955]
Slc43a3 1.3189002 0.0004700 solute carrier family 43, member 3 [Source:MGI Symbol;Acc:MGI:1931054]
Slc48a1 0.6300636 0.0305495 solute carrier family 48 (heme transporter), member 1 [Source:MGI Symbol;Acc:MGI:1914989]
Slc4a2 0.6228396 0.0174332 solute carrier family 4 (anion exchanger), member 2 [Source:MGI Symbol;Acc:MGI:109351]
Slc4a5 -2.6991249 0.0041480 solute carrier family 4, sodium bicarbonate cotransporter, member 5 [Source:MGI Symbol;Acc:MGI:2443220]
Slc4a7 -1.1477270 0.0001308 solute carrier family 4, sodium bicarbonate cotransporter, member 7 [Source:MGI Symbol;Acc:MGI:2443878]
Slc4a8 -1.3471033 0.0000487 solute carrier family 4 (anion exchanger), member 8 [Source:MGI Symbol;Acc:MGI:1928745]
Slc52a2 0.6695203 0.0125906 solute carrier protein 52, member 2 [Source:MGI Symbol;Acc:MGI:1289288]
Slc5a3 -1.2562283 0.0336439 solute carrier family 5 (inositol transporters), member 3 [Source:MGI Symbol;Acc:MGI:1858226]
Slc6a19 -1.5934789 0.0000984 solute carrier family 6 (neurotransmitter transporter), member 19 [Source:MGI Symbol;Acc:MGI:1921588]
Slc6a9 2.1985085 0.0000000 solute carrier family 6 (neurotransmitter transporter, glycine), member 9 [Source:MGI Symbol;Acc:MGI:95760]
Slc7a1 0.8250923 0.0193088 solute carrier family 7 (cationic amino acid transporter, y+ system), member 1 [Source:MGI Symbol;Acc:MGI:88117]
Slc7a11 3.8804610 0.0000000 solute carrier family 7 (cationic amino acid transporter, y+ system), member 11 [Source:MGI Symbol;Acc:MGI:1347355]
Slc7a3 2.2430652 0.0000000 solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 [Source:MGI Symbol;Acc:MGI:1100521]
Slc7a5 1.0617126 0.0003489 solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 [Source:MGI Symbol;Acc:MGI:1298205]
Slc9a5 -1.7304090 0.0000000 solute carrier family 9 (sodium/hydrogen exchanger), member 5 [Source:MGI Symbol;Acc:MGI:2685542]

Mitochondria mention in gene description

gene log2FoldChange padj description
Acaa2 -0.6030473 0.0231411 acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase) [Source:MGI Symbol;Acc:MGI:1098623]
Aldh2 -0.6155486 0.0155190 aldehyde dehydrogenase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:99600]
Atp5g1 1.1870390 0.0000436 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C1 (subunit 9) [Source:MGI Symbol;Acc:MGI:107653]
Bcat2 0.7628810 0.0016462 branched chain aminotransferase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1276534]
Car5b -1.3287664 0.0246614 carbonic anhydrase 5b, mitochondrial [Source:MGI Symbol;Acc:MGI:1926249]
Clic4 0.9727174 0.0006774 chloride intracellular channel 4 (mitochondrial) [Source:MGI Symbol;Acc:MGI:1352754]
Clpx 0.5981059 0.0263593 caseinolytic mitochondrial matrix peptidase chaperone subunit [Source:MGI Symbol;Acc:MGI:1346017]
Decr1 0.5780524 0.0494988 2,4-dienoyl CoA reductase 1, mitochondrial [Source:MGI Symbol;Acc:MGI:1914710]
Ears2 1.1988671 0.0006042 glutamyl-tRNA synthetase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1914667]
Grpel2 0.5371752 0.0409241 GrpE-like 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1334416]
Lonp1 1.3595610 0.0000000 lon peptidase 1, mitochondrial [Source:MGI Symbol;Acc:MGI:1921392]
Mecr 0.5573707 0.0283347 mitochondrial trans-2-enoyl-CoA reductase [Source:MGI Symbol;Acc:MGI:1349441]
Metap1d 0.9141497 0.0014668 methionyl aminopeptidase type 1D (mitochondrial) [Source:MGI Symbol;Acc:MGI:1913809]
Micos13 0.5907215 0.0435347 mitochondrial contact site and cristae organizing system subunit 13 [Source:MGI Symbol;Acc:MGI:2442174]
Mpc2 0.9387232 0.0041623 mitochondrial pyruvate carrier 2 [Source:MGI Symbol;Acc:MGI:1917706]
Mrm3 1.0555920 0.0011480 mitochondrial rRNA methyltransferase 3 [Source:MGI Symbol;Acc:MGI:1914640]
Mrpl12 0.6460569 0.0357102 mitochondrial ribosomal protein L12 [Source:MGI Symbol;Acc:MGI:1926273]
Mrpl15 0.6862601 0.0260657 mitochondrial ribosomal protein L15 [Source:MGI Symbol;Acc:MGI:1351639]
Mrpl20 1.1192202 0.0000948 mitochondrial ribosomal protein L20 [Source:MGI Symbol;Acc:MGI:2137221]
Mrpl24 0.7085136 0.0047444 mitochondrial ribosomal protein L24 [Source:MGI Symbol;Acc:MGI:1914957]
Mrpl35 0.9801261 0.0020712 mitochondrial ribosomal protein L35 [Source:MGI Symbol;Acc:MGI:1913473]
Mrpl38 0.6559809 0.0167670 mitochondrial ribosomal protein L38 [Source:MGI Symbol;Acc:MGI:1926269]
Mrpl46 0.9583535 0.0047198 mitochondrial ribosomal protein L46 [Source:MGI Symbol;Acc:MGI:1914558]
Mrpl49 0.6342004 0.0467517 mitochondrial ribosomal protein L49 [Source:MGI Symbol;Acc:MGI:108180]
Mrpl52 1.0129901 0.0000636 mitochondrial ribosomal protein L52 [Source:MGI Symbol;Acc:MGI:1916086]
Mrpl54 0.7524919 0.0209862 mitochondrial ribosomal protein L54 [Source:MGI Symbol;Acc:MGI:1913297]
Mrpl55 0.7439040 0.0176261 mitochondrial ribosomal protein L55 [Source:MGI Symbol;Acc:MGI:1914462]
Mrpl57 0.6619004 0.0414668 mitochondrial ribosomal protein L57 [Source:MGI Symbol;Acc:MGI:1915090]
Mrpl58 0.7522415 0.0075562 mitochondrial ribosomal protein L58 [Source:MGI Symbol;Acc:MGI:1915822]
Mrps12 0.7076244 0.0208072 mitochondrial ribosomal protein S12 [Source:MGI Symbol;Acc:MGI:1346333]
Mrps14 0.9010184 0.0022932 mitochondrial ribosomal protein S14 [Source:MGI Symbol;Acc:MGI:1928141]
Mrps17 0.5349370 0.0468114 mitochondrial ribosomal protein S17 [Source:MGI Symbol;Acc:MGI:1913508]
Mrps18a 0.7555201 0.0061968 mitochondrial ribosomal protein S18A [Source:MGI Symbol;Acc:MGI:1915815]
Mrps18b 0.8453307 0.0283545 mitochondrial ribosomal protein S18B [Source:MGI Symbol;Acc:MGI:1914223]
Mrps2 0.7519048 0.0296977 mitochondrial ribosomal protein S2 [Source:MGI Symbol;Acc:MGI:2153089]
Mrps22 0.9502394 0.0133136 mitochondrial ribosomal protein S22 [Source:MGI Symbol;Acc:MGI:1928137]
Mrps24 0.5830597 0.0165074 mitochondrial ribosomal protein S24 [Source:MGI Symbol;Acc:MGI:1928142]
Mrps26 0.7661575 0.0053349 mitochondrial ribosomal protein S26 [Source:MGI Symbol;Acc:MGI:1333830]
Mrps28 1.2509283 0.0023886 mitochondrial ribosomal protein S28 [Source:MGI Symbol;Acc:MGI:1913480]
Mrps6 0.6661240 0.0293529 mitochondrial ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:2153111]
Mss51 -1.0965640 0.0405396 MSS51 mitochondrial translational activator [Source:MGI Symbol;Acc:MGI:1922093]
Mtfr2 -1.5148135 0.0131970 mitochondrial fission regulator 2 [Source:MGI Symbol;Acc:MGI:1919054]
Mtg1 0.6282553 0.0224446 mitochondrial ribosome-associated GTPase 1 [Source:MGI Symbol;Acc:MGI:2685015]
Mtg2 0.8143426 0.0008459 mitochondrial ribosome associated GTPase 2 [Source:MGI Symbol;Acc:MGI:106565]
Mtrfr 0.9353115 0.0014219 mitochondrial translation release factor in rescue [Source:MGI Symbol;Acc:MGI:1919900]
Rars2 1.3563843 0.0000012 arginyl-tRNA synthetase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1923596]
Shmt2 1.0733335 0.0093724 serine hydroxymethyltransferase 2 (mitochondrial) [Source:MGI Symbol;Acc:MGI:1277989]
Slc25a1 -1.1896109 0.0000137 solute carrier family 25 (mitochondrial carrier, citrate transporter), member 1 [Source:MGI Symbol;Acc:MGI:1345283]
Slc25a15 0.7708455 0.0081739 solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15 [Source:MGI Symbol;Acc:MGI:1342274]
Slc25a20 0.5879487 0.0238877 solute carrier family 25 (mitochondrial carnitine/acylcarnitine translocase), member 20 [Source:MGI Symbol;Acc:MGI:1928738]
Slc25a23 -1.4187696 0.0000538 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23 [Source:MGI Symbol;Acc:MGI:1914222]
Slc25a25 -0.7660400 0.0418809 solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 25 [Source:MGI Symbol;Acc:MGI:1915913]
Slc25a5 -0.8637030 0.0036617 solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5 [Source:MGI Symbol;Acc:MGI:1353496]
Tefm 0.9089343 0.0106374 transcription elongation factor, mitochondrial [Source:MGI Symbol;Acc:MGI:1915800]
Timm13 0.6800608 0.0490480 translocase of inner mitochondrial membrane 13 [Source:MGI Symbol;Acc:MGI:1353432]
Timm50 0.8750085 0.0162373 translocase of inner mitochondrial membrane 50 [Source:MGI Symbol;Acc:MGI:1913775]
Tk2 0.6726566 0.0169575 thymidine kinase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:1913266]
Tomm40 0.8864587 0.0356209 translocase of outer mitochondrial membrane 40 [Source:MGI Symbol;Acc:MGI:1858259]
Tomm5 0.8156831 0.0291215 translocase of outer mitochondrial membrane 5 [Source:MGI Symbol;Acc:MGI:1915762]
Tusc2 1.1708899 0.0002552 tumor suppressor 2, mitochondrial calcium regulator [Source:MGI Symbol;Acc:MGI:1931086]